new branch
BG with permutations
continue refactoring
it works with permutations
sibelia incorporated
iterative
fasta output
minor fix
readme and examples added
output dirs
small ifx
Update USAGE
README improvements.
Applying markdown to readme files.
Usage minor.
Python 2.6 minor.
test script with multiple references
debrujin refinement
debug output
fixed huge phylogeny bugs